适应性免疫受体库群落作为大型免疫学数据的公平信息和知识管理模型。
The adaptive immune receptor repertoire community as a model for FAIR stewardship of big immunology data.
作者信息
Scott Jamie K, Breden Felix
机构信息
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
出版信息
Curr Opin Syst Biol. 2020 Dec;24:71-77. doi: 10.1016/j.coisb.2020.10.001. Epub 2020 Oct 10.
Abstract
Systems biology involves network-oriented, computational approaches to modeling biological systems through analysis of big biological data. To contribute maximally to scientific progress, big biological data should be FAIR: findable, accessible, interoperable, and reusable. Here, we describe high-throughput sequencing data that characterize the vast diversity of B- and T-cell clones comprising the adaptive immune receptor repertoire (AIRR-seq data) and its contribution to our understanding of COVID-19 (coronavirus disease 19). We describe the accomplishments of the AIRR community, a grass-roots network of interdisciplinary laboratory scientists, bioinformaticians, and policy wonks, in creating and publishing standards, software and repositories for AIRR-seq data based on the FAIR principles.
摘要
系统生物学涉及通过分析大量生物学数据，采用面向网络的计算方法对生物系统进行建模。为了最大程度地推动科学进步，大量生物学数据应具备FAIR原则：可查找、可访问、可互操作和可重复使用。在此，我们描述了高通量测序数据，这些数据表征了构成适应性免疫受体库的B细胞和T细胞克隆的巨大多样性（抗原受体库测序数据）及其对我们理解2019冠状病毒病（COVID-19）的贡献。我们描述了抗原受体库社区（一个由跨学科实验室科学家、生物信息学家和政策专家组成的基层网络）在基于FAIR原则创建和发布抗原受体库测序数据的标准、软件和存储库方面所取得的成就。
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BMC Med Res Methodol. 2021 Jun 5;21(1):117. doi: 10.1186/s12874-021-01304-y.
2
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Cell Rep. 2021 May 25;35(8):109173. doi: 10.1016/j.celrep.2021.109173. Epub 2021 May 9.
3
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4
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Elife. 2021 Jan 5;10:e63502. doi: 10.7554/eLife.63502.
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